back in the early 90s i changed the fork lowers on my 72 CB750 for CB900 ones so i could use better calipers (a pair of 4 piston early GSXR ones), then i came up against the same problem you did above, the spokes hit the back of the caliper (those GSXR calipers eventually found a happy home up the front of my Vmax where they do a hell of a better job than the crap Mr Yamaha saw fit to issue back in 1988. thats them in the pic on the left)
i ended up finding a pair of twin piston sliding caipers (from a VF750 from memory), because the pistons were both on the outside of the wheel the back of the caliper was thin enough to clear the spokes.
obviously a pair of VF calipers is not the answer to your problem but its entirely likely that there are calipers out there with the correct bolt spacing that only have the pistons on the outside, probably from some more basic model than a GSXR.
i understand that you're after the ultimate braking that you can get but when you consider the stock CB single piston single caliper you're replacing it's maybe worth a look. i'm currently building another CB750 and it'll be getting CB900 forks and better brakes like last time